im_sort: A function to sort image paths for large imaging datasets

In sgoldenlab/SMART: SMART (Semi-manual alignment to reference template): a pipeline for whole brain mapping projects

A function to sort image paths for large imaging datasets

Description

User friendly way to sort images from the registration channel. Asks for user input to account for flexible naming conventions for images.

Usage

im_sort(setup, extension = "tif", separator = "_", position = NULL)

Arguments

setup	(required) Argument used to access registration and segmentation folders.
extension	(optional, default = "tif") File extension of the imaging data.
separator	(optional, default = "_") Separator character to parse filename.
position	(optional) Position of z number in filename. If this argument is called, the user input is skipped.

Details

Compared to the list.files() function, this function will sort 100+ files in their appropriate order by z plane.

Value

setup is returned with setup$image_paths filled as a list of sorted paths. The first element is a sorted character vector of registration channel paths. The second element is a sorted character vector of segmentation channel paths.

sgoldenlab/SMART documentation built on March 20, 2022, 5:16 p.m.